Bioinformatics Engineer
Full-stack bioinformatics. Expert in pipelines for large-scale genomic analysis, software, and web-portal infrastructure to store, manage, process and exploit omics data.
Now: leading the CIBERINFEC bioinformatics platform and building Omilinx. Open to projects and collaborations.
01 Projects
Network work, open source and things of my own. Filter by type.
Technical lead of the platform: researcher support, workflows, infrastructure, documentation, training and cross-group collaboration across the network.
Rollout and adoption of the shared HPC: requirements, initial setup, coordination, testing, user onboarding, pipeline adaptation and documentation.
Platform integrating genomic data and metadata for pathogen research and surveillance: API, ETL, normalisation, permissions, web UI and deployment.
The API layer of the PathoCore ecosystem: REST endpoints, OMOP mapping, data validation and normalisation, permissions and schema versioning.
Bacterial assembly and annotation for short, long or hybrid reads: quality control, assembly, polishing, taxonomic classification and annotation in a single flow.
Large-scale study of the microRNAs involved in hepatitis C infection in HIV patients and their relationship with the viral reservoir.
Functional enrichment from validated microRNA–target interactions: the user brings a miRNA list and gets pathways, networks and tables back.
My own platform to centralise omics projects, samples, metadata, QC, runs and results with full traceability. In active development.
Public dataset analysis on diabetes: QC, integration, clustering and annotation of cell types, glycocalyx genes and angiogenesis.
My own training initiative in applied bioinformatics: hands-on courses on pipelines, HPC, R and reproducible analysis.
AI assistants running inside the lab, with no data leaving it: support for day-to-day analysis, documentation and code.
Working agents that take over a project's repetitive tasks and leave the result ready to review.
02 Services
Three pieces, hired together or separately: pipelines, backend and Omilinx.
I run Nextflow and nf-core pipelines on real infrastructure — HPC or cloud — validated against control data, with pinned versions before anything reaches production.
I design the APIs, databases and data models behind it: OMOP-mapped, standardised, and built to keep working as the data grows.
I set up the infrastructure to deploy your pipelines, then put the results in front of your whole lab through a GUI — no code required.
03 Path
From thesis to platform — always the same thread.
04 Open source
Software I maintain or contribute to, in public and versioned.
| Project | My role | Link |
|---|---|---|
| nf-core/bacass maintainer | Maintaining and developing the bacterial assembly & annotation pipeline: releases, PR review and community support. | nf-co.re ↗ |
| relecov-tools contributor | Contributions to the genomic surveillance data-processing software, including background execution of the wrapper (--background, --nohup). | github ↗ |
| CORALIS author · R | My own R package for ncRNA enrichment based on validated interactions. | github ↗ |
| nf-core community organiser · Madrid | Organiser of the Madrid node at nf-core hackathons, as well as participant. | nf-co.re ↗ |
05 Community
InCoB / ISCB-APAC 2026 · Penang
Modular architecture, data model and sharing flow for genomic surveillance.
Royale Chulan, Penang
25th international bioinformatics conference and the first ISCB-Asia Pacific.
CNM · Majadahonda, Madrid
Organiser of the Madrid node: viralrecon and bacass, on site and online.
AIDS 2022 · Montreal
C14MC cluster dysregulation in HIV patients by HCV exposure, with sex bias.
Hands-on courses for research teams: Nextflow, HPC and single-cell analysis.
Online courses ↗| Course | Where | Length |
|---|---|---|
| R programming and statistical analysis for clinical and biomedical researchers | CIBERINFEC | hands-on |
| HPC — basic, intermediate and advanced | CIBERINFEC | 3 levels |
| Nextflow | CIBERINFEC | hands-on |
| Python packaging | E-learning | in prep |
| Retina & glycocalyx scRNA-seq (Scanpy) | E-learning | in prep |
06 Stack